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OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

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Figure 1: SWATH-MS data-independent acquisition and OpenSWATH analysis.
Figure 2: Identification and quantification accuracy of OpenSWATH on the SGS data set.
Figure 3: Streptococcus pyogenes exposed to human plasma (0% plasma versus 10% plasma).

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Acknowledgements

H.L.R. was funded by ETH (ETH-30 11-2), G.R. and S.M.M. were funded by the Swiss Federal Commission for Technology and Innovation CTI (13539.1 PFFLI-LS), P.N., L.G. and R.A. were funded by the advanced European Research Council grant Proteomics v3.0 (233226), L.G. and R.A. were funded by PhosphonetX project of SystemsX.ch, J.M. was funded by the Swedish Research Council (project 2008-3356), the Crafoord Foundation (20100892) and the Swedish Foundation for Strategic Research (FFL4). Further funding was provided to R.A. by the Swiss National Science Foundation. We would like to thank the SyBIT project of SystemsX.ch for support and maintenance of the lab-internal computing infrastructure, the ITS HPC team (Brutus) and the OpenMS developers for including OpenSWATH in the OpenMS framework and fixing MS Windows compatibility bugs.

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Author notes

  1. Hannes L Röst and George Rosenberger: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

    Hannes L Röst, George Rosenberger, Pedro Navarro, Ludovic Gillet, Saša M Miladinović, Olga T Schubert, Ben C Collins, Lars Malmström & Ruedi Aebersold

  2. PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland

    Hannes L Röst, George Rosenberger & Olga T Schubert

  3. Biognosys AG, Schlieren, Switzerland

    Saša M Miladinović

  4. SyBIT project of SystemsX.ch, ETH Zurich, Zurich, Switzerland

    Witold Wolski

  5. Department of Immunotechnology, Lund University, Lund, Sweden

    Johan Malmström

  6. Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland

    Ruedi Aebersold

  7. Faculty of Science, University of Zurich, Zurich, Switzerland

    Ruedi Aebersold

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  1. Hannes L Röst
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  2. George Rosenberger
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Correspondence to Ruedi Aebersold.

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Competing interests

J.M. is co-founder and board member of Biognosys AG. J.M. and R.A. hold shares of Biognosys AG, which operates in the field covered by the article. The research group of R.A. is supported by AB SCIEX by providing access to prototype instrumentation.

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Röst, H., Rosenberger, G., Navarro, P. et al. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol 32, 219–223 (2014). https://doi.org/10.1038/nbt.2841

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